Going abreast of high public concerns on the environment, the need of environmental modeling has been increased to assess the impact of space exploitation of environment. GIS offers potential solutions to the many problems encountered during water-quality modeling. But there are also many problems associated with the modeling. The preparation of necessary parameters for the modeling can be complicated. Also, the results from one model can be different from each other even the same area is analyzed. This paper aims to develop the data processing system to couple the Qual2E and HyGIS in which Qual2E input and output data files can be created, modified and processed using HyGIS and assess the performance of the system. A structural analysis and standardization of modeling are conducted to identify data flow and processing of Qual2E. Algorithms of the defined processors are designed and developed as component modules. The data model of HyGIS-Qual2E is designed, and GUI(Graphical User Interface) is developed using Visual Basic 6.0 and GDK.